4KTX

Crystal structure of the catalytic domain of botulinum neurotoxin BoNT/A C134S mutant with covalent inhibitor that modifies Cys-165 causing disorder in 167-174 stretch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Covalent modification of the active site cysteine stresses Clostridium botulinum neurotoxin A

Guitot, K.Vera, L.Le Roux, L.Bregant, S.Ptchelkine, D.Beau, F.Stura, E.A.Dive, V.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Botulinum neurotoxin A light chainA445Clostridium botulinum A str. HallMutation(s): 1 
Gene Names: botACBO0806CLC_0862bna
EC: 3.4.24.69
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Explore P0DPI1 
Go to UniProtKB:  P0DPI1
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide inhibitor MPT-DPP-ARG-G-LEU-NH2B6synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

Download Ideal Coordinates CCD File 
D [auth A]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DPP
Query on DPP
BL-PEPTIDE LINKINGC3 H8 N2 O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.207 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.41α = 90
b = 65.41β = 90
c = 200.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
DNAdata collection
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Advisory, Data collection, Derived calculations, Refinement description, Source and taxonomy